How do size-expanded DNA nucleobases enhance duplex stability? Computational analysis of the hydrogen-bonding and stacking ability of xDNA bases

Journal of Physical Chemistry B

Volumn 111, Issue 11, 2007, Pages 2999-3009

  McConnell, Tom L ^a   Wetmore, Stacey D ^b  

^a MOUNT ALLISON UNIVERSITY   (Canada)

^b UNIVERSITY OF LETHBRIDGE   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

BENZENE; BINDING SITES; HYDROGEN BONDS; MATHEMATICAL MODELS; NATURAL SCIENCES COMPUTING;

BENZENE SPACERS; COMPUTATIONAL CHEMISTRY; HYDROGEN-BONDING PROPERTIES; NUCLEOBASES;

DNA;

EID: 34047248888     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp0670079     Document Type: Article

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96. -1) prefer a vertical separation distance of 3.4 Å.
97. 2 sequences considered were ATCG, ATTA, and GCGC where slightly larger deviations were found for the guanine-cytosine interactions.
98. -1) in stacking interactions that should be the same (i.e., two intrastrand T:xA interactions in (TxA):(xAT) sequence). These differences likely arise because of slight errors in our method for finding the center of the base pairs. Since none of the differences are significant enough to detract from our main conclusions, we report the calculated interactions for each quadruplet for consistency and clarity.